Mass Effect: Sins of the Father
by UCryWolFe
Summary: Mass Effect AU. One bad decision between adults leaves unanswered questions for their children, and worlds will come crashing down. Is the truth really so bad, though?
1. Prologue

**A/N: Hello yon reader! This is my first ME fanfic. It is AU, but elements of canon will be there, just out of order, severely out of order. Enjoy~**

**Mass Effect – Prologue**

* * *

_He breathed in the raven-haired man's scent as their tongues explored each others. _

_Kaidan. That was his name._

_He tugged Kaidans head back, nipping at various spots along the mans neck. Each kiss and nip earned him a soft moan from the man._

_Kaidans hands eventually drug his lips back to Kaidans own, their tongues once more embracing as if two lovers having parted._

_His hands explored Kaidan's body, tugging the shirt up to press against the bare skin that had goosebumps crawling over it. His skin was warm, and his fingers continued to dance over the mans muscled stomach before Kaidan finally gave in to temptation and dragged the man home for the night._

_Said night was actually three nights._

_Three nights of bliss, wrapped together, exploring each other repeatedly, sometimes with animalistic fury and other times with a gentle grace._

_Then it was over. Kaidan had never bothered to learn his name, but even the man who walked out of Kaidans apartment didn't seem to mind. He knew he would never love Kaidan, and Kaidan didn't seem interested in anything more than what had happened when they did almost nothing but use each other for release._

_Granted, his mother on the other hand was furious when he returned. Her gray hair was partly(well….mostly) his fault. He did give her a kiss on the cheek as he returned though, even if she didn't fall for it one bit._

"_Andrew Jacob, I swear you are going to be the death of me! Is that what you want to put your mother through?"_

_He dropped his coat on the couch before turning to face her, knowing well at this point to just let her fuss and worry._

_Eventually, after a headache was threatening to build he pointed out, "Mother, I -am- 26. I would at least like some allotted freedom if I am to stay here, if just for a short time." _

_She sighed, not out of frustration but out of worry. He'd long since grown accustomed to this. She looked like she was about to say something when the door rang. She moved for the door, and instinctively, he followed. When she opened the door she brightened immediately since she warmly greeted their caller._

"_Well, it's about time you showed up! Come on in!"_

_She greeted the man that walked in with a hug, stating, "I don't think you've met my son. This is Andrew Jacob, but he makes such a fuss about wanting to be called A.J." She couldn't help but give a light chuckle as A.J. shook the strangers hand._

"_Hello." _

_The stranger replied, "Hello, A.J. My name is Captain Anderson."_

_A.J. would just nod before moving aside to let both Anderson and his mother move on inside. As for A.J. himself he decided to bail, if just for a little while to give the two of them a bit of space. "Heading out, back in a tick."_

_He heard his mother shout something about needing to bring groceries so he added that to his mental checklist._

_On the way however a strange woman stepped in his path._

_His head tilted slightly before the woman held out an envelope, "This is for you, A.J."_

"_What?" He took the envelope curiously before opening it. It looked like some sort of invitation. He then looked back to the woman who introduced herself, "My name is Janet, Mr. Chakwas. And I have heard you are looking for work. I'm here today on behalf of the owner to make you an offer."_

_A.J. frowned slightly, not having yet made it known he was looking for work(again) but as he looked back to the envelope he noticed a bright, emblazoned capital 'C' on the front._

"_Curious." He couldn't help but take the bait, looking to the woman once more, "Might I ask what kind of offer….?"_

* * *

_A.J. stared at the facility around him, people bustling back and forth as the woman from earlier, Janet, gave him a brief tour. Finally she stopped in front of a door before looking to A.J. She then held out a package for him saying, "This is your new room, and this is your uniform. We will come for you in one hour to start your training. Welcome aboard."_

_He nodded before heading inside the room, finding it surprisingly spacious, with the minimalist of necessities one would need. He laid the package down before extracting the uniform, eying the yellow and white that adorned it._

"_Finally, something to make her proud of."_


	2. Chapter 1 - Brand New Day

**A/N: Chaptuh 1! Rinse! Read! Review! **

**Chapter 1: Brand New Day(Pt. 1)**

* * *

_Tick. Tock. Tick Tock._

A.J. sighed to himself as he stared at the screen in front of him. Notes, reports, graphs, and all manners of charts flashed across the screen, each demanding his attention as much as the previous and the next. He didn't feel too inclined to pay much mind to them, however. His thoughts were elsewhere, on a certain call home he was liable to be reprimanded for. He didn't care though, but the more he heard the ancient clock ticking the more he silently cursed his roommate who had thought it a good idea to purchase the blasted thing.

The man would just run a hand through his dirty blond hair before leaning back in his chair to stretch. His shift was already over but he stayed every so often to try and finish up more work. Lately though, he got the strange feeling that he was being watched. Usually he was ignored and left to his own devices, however he couldn't help this little feeling that more eyes were on him lately. Well, more than usual. He'd then stand up, arching his back to relive some of the tension that had built up, and when the few small pops made themselves heard he sighed.

A.J. was tired beyond belief for some reason today. It seemed he had done more than anticipated, but he didn't like procrastinating. After his somewhat disastrous call home earlier he decided it would be easier to just do a bit more work, but for the last half-hour since his shift had finished A.J. had basically stared at a computer screen.

His omni-tool suddenly lit up, indicating he had a new message, and while he never cared much for the thing he did see the benefits that came with having one. He flicked through the messages till he found the new message that he had just received. _'Well now, this is rather unexpected.' _This was the first line of thought that came through his mind as he saw who the message was from.

The sender was The Illusive Man himself.

A.J. thought more to himself before actually reading the message. Thankfully, the message was short and to the point.

**Dr. Chakwas,**

**Pack your things immediately. You have a new assignment that will cause you to be mobile. Report to the hangar in 30 minutes.**

** Illusive Man**

* * *

A.J. stood at the door to the hangar with 2 minutes left to spare, wondering if he was actually being giving a new assignment or if his contract was being terminated. That last thought sent an involuntary shiver up his spine. There were enough rumors going around to suggest what truly happened when a contract with Cerberus was terminated. He had worked with them for a little over three years now, and had seen a few faces disappear in that time to haphazard a guess.

Still, he wasn't going to find out until he entered the hangar, now was he? His two minutes now up and having been spent in a train of thought that had since derailed he stepped through the door to see quite the surprise.

It easily had to be one of the most impressive ships he had ever seen, and that was just on the outside. He couldn't help but study the ship, eyes wandering over it fully before seeing SR-2 on its side. He raised a curious brow before walking closer. About fifty feet away is when he received a beep, signaling that he had a call this time.

"Dr. Chakwas speaking." It was normally how he answered a call, but the voice responding didn't seem to care. A straightforward reply was given, "Dr. Chakwas. Welcome to your new assignment. This is the SSV Normandy."

A.J. stared before greeting, "Sir, how long will I be serving under this new post?" He couldn't help but admit that he was intrigued. Traveling the stars was something he never got to do often and now this situation was just dropped in his lap. It was like a prayer about boredom had been answered.

"Unknown. That will be up to the Commander. Your role is to ensure the crew stays healthy and alive as any normal doctor."

A.J. had no response to that beyond, "Understood, sir." He did sigh internally, the situation thankfully not being drastic. Plus, he was finally getting recognition!

"Dr. Chakwas, you were not my first choice for this task. I originally chose your mother, however she insisted that you take this opportunity. So don't fail me, failure is -not- an option."

He gave a nod of acknowledgement followed by, "Understood." Silently, he cursed that woman, yet had to be grateful. Damn! She always somehow managed to do….-that-. He wasn't a parent yet so he just didn't understand.

The Illusive Man simply stated, "Commander Shephard is on his way. Report to the ship and make sure the crew is in peak condition." His omni-tool then beeped letting him know the call was over. He ran a hand through his blond hair before sighing, outwardly this time.

He picked up his gear, which was mostly uniforms, a handgun, twin swords, and a few miscellaneous items before entering the ship. He did pass various others he recognized, like Ms. Chambers and the engineer duo Kenneth and Gabriella, who seemed surprised to see him but greeted him all the same. He had a few moments of idle chat with them each before finally entering the medbay. Needless to say, he was impressed. Aside from being well stocked and organized there was also a space in the back for him.

Granted it housed the server core but it was a place of his own, so he was okay with that. While he was getting set up he noticed a holo-monitor and then a disembodied voice greeting him, "Welcome to the Normandy, Dr. Chakwas."

A.J. stopped in front of the image that appeared, a glowing orb with lines going through it, giving it an almost ominous look. The doctor would just tilt his head before leaning close to examine what he assumed was the ships VI, "Thank you. You are the ships VI?"

"I'm afraid you are mistaken, Dr. Chakwas. I am the Normandy's AI. I am called the Enhanced Defense Intelligence, or E.D.I. for short."

"EDI? Interesting." He'd give a brief smile before turning to survey the medbay as EDI chimed in, "Do you have any questions about the medbay, or the staff serving aboard the Normandy? Their dossiers are available upon request."

A.J. would then smile to EDI before shaking his head, "I should get my bearings first. I would like to go over them in due time, but I trust that if there is something that I must immediately be informed of you will let me know?"

"Of course, doctor." EDI's image then disappeared, leaving A.J. alone as he had requested. He'd then sigh before running a hand through his dirty blonde hair. If anyone knew his mother then they knew his hair was a stark contrast from her own. Then again, her hair was graying.

He'd blink, realizing his thoughts were running away again and he needed time to get accustomed to his new surroundings. Thankfully the inventory was fully stocked so that was something he could cross off his mental checklist. He did take a small bit of time to adorn his twin swords on one of the walls, smiling as he did so.

He stared at them, memories flooding back through his mind the more he looked at them. Finally, he'd let out a depressed sigh before moving out to the cafeteria to grab a cup of coffee. Rupert had a cup whipped up for him in no time flat and right as A.J. was taking a sip Rupert decided to initiate conversation, "So, looks like we're about to meet the infamous Commander Shephard. I wonder what he's like."

A.J. first had to fight hard not to spit out the gruel that Rupert had served him as 'coffee'. Second A.J. took a moment to think over the situation before giving a shrug, "If you're looking to stories to label a man then I doubt you will find the truth. I suggest asking him when you see him." Rupert would just give a hearty laugh before chatting idly. A.J. chatted along with Rupert for five or so minutes, at least taking a step to make friends, even if people avoided him. Ah well. He thanked Rupert for the coffee, daring another sip and avoiding a shudder before trekking back over to the medbay.

As the doors slid open he saw a male figure standing in the middle of the medbay, donned in armor with an adorned N7 logo. The doctor walked forward to his desk, taking care to set his coffee down with a mental thought to dispose of the hideous coffee later before looking up to see the last person he was expecting. At least, this soon.

"Commander Shephard?" The curiosity in A.J.'s voice was almost a content purr as the dirty blond stared back before returning the greeting, "You're the doctor for the new Normandy? Funny, I was told that Dr. Chakwas would be down here."

A.J. really, -really-, had to work not to frown at that statement. He was used to being compared(or mistaken for) his mother. So he just gave an annoyed sigh before correcting Shephard, "You are speaking to Dr. Chakwas, Commander." Seeing the confused look on the commanders face had the doctor wanting to headbutt a Krogan. Instead, he elaborated, "The Dr. Chakwas you know is my mother. I happened to follow in the family business as well."

The commander gave A.J. a surprising nod before again surprising A.J. with his next statement, "Then welcome aboard the Normandy Dr. Chakwas." This surprised the young doctor. The only other person to have welcomed A.J. aboard was EDI. Surprising, and intriguing.

The doctor would smile before nodding, "Thank you, Commander." He'd then pull up his omni-tool and start running a diagnostic while explaining that he was doing just that.

"A check-up? Do I look like I'm still in bad shape?" was the Commanders first response. A.J. would just shake his head before pointing out, "I'm actually checking your implants. I want to see if your body is showing signs of rejection." He did another sweep of Shephards body before nodding at the positive results on his omni-tool. "Impressive. No sign of rejection, and you're almost fully healed, minus the scarring on your face." Shephard raised a hand to his face before A.J. tilted his head, "Is something wrong, Commander?"

Shephard looked to the doctor before asking, "Will the scars heal? Or do I need surgery?"

The blonde gave Shephard a nod in return before motioning the commander over to his desk. He pulled out a mirror before handing it over to the Commander as he stated, "That depends on you, actually. Scars heal naturally, depending on the outlook you choose to have." Internally A.J. sighed since he had a feeling he was about to sound like his mother about this topic, but he had been asked, "If you choose to have a positive outlook, making good choices, etcetera, then your scars will heal all on their own with no surgery needed. However, if you choose the opposite by making bad decisions then your scars won't heal."

The Commander looked perplexed before A.J. added, "There is an upgrade for the medbay you can get which would provide the tools necessary for the surgery, should that be the route taken."

Shephard nodded before looking over his scars in the mirror. The commander tilted his head back and forth, surveying each scar before handing the mirror back, "Noted. Is there anything else I need to know?" The doctor simply shook his head before the commander once again surprised him, "Well, is there anything you need?"

A.J. blinked once before the corners of his mouth tugged upwards, though only barely, as he said, "The medbay is fully stocked at the moment so I will have little difficulty tending to the needs of the Normandy crew." Shephard folded his arms across his broad chest as he then reiterated, "Okay, then is there anything specific you yourself need?" A.J. was apparently not going to stop being surprised by this man. Scrutinizing as the doctor was he couldn't deny that the man seemed sincere. Finally, after realizing that there had been an awkward silence the doctor would 'hmm' before inquiring, "Mother seems to almost faun over Serrice Ice Brandy. I myself have never tried it but if you happen to find a store that sells it could you let me know? I might as well try it to see what kind of spell that brandy has on that woman."

Shephard merely grinned before uncrossing his arms, "I'll do you one better. If I find a bottle I'll bring it to you." The commander even gave a brief smile while A.J. was already shaking his head, then insisted, "It's no trouble. I'll pay for it."

Shephard just narrowed his eyes before remarking, "Don't worry about it." His tone suggested a finality to the topic, and A.J. happened to pick up on it. Internally, he frowned, but dropped it in favor of not making his new superior mad. Instead he'd nod, mumble a brief thanks before asking, "Is there something else I can help you with?" He did give a small smile, trying to be somewhat friendly, but Shephard just waved him off, "I'm fine." A.J. then gave another nod saying, "See you soon, Commander."

The doctor then planted himself in his chair before turning around to review more charts. He then slowly became aware of one thing: Commander Shephard hadn't left the medbday. Then again, Shephard did have just about every right to be here. The Illusive Man made it abundantly clear(multiple times) that this was Shephards ship, and that's how it was going to be. His thoughts ran away with themselves before he heard footsteps then the medbay doors opening and closing. He sighed, externally this time before muttering, "Horrible first impression." He'd then clamp down on the bridge of his nose briefly with two fingers before settling for rubbing his temples simultaneously.

With luck, this day would be over soon.

It was then that he heard the comm come on and the pilot, Joker, speak, "Actually, doc, I've heard worse first impressions. At least you didn't crash and burn, so that counts for something!"

A.J. would just groan before tapping his head repeatedly against the desktop.

And the day had only just begun.

* * *

**A/N: Hullo! Laziness reared its ugly head and…yeah. Still in the dark on if I'm wanting to do multiple POV or single POV each chapter so this next chapter will have multiple POV to see if it works out better. Laziness, away! Read & review, if you'd be so kind.**


	3. Chapter 1 - Brand New Day(Pt 2)

**A/N: Chapter 2 up! Read, review, uh, stuff!**

**Chapter 1: Brand New Day(Pt. 2)**

* * *

Shephard sighed as he leaned against the outside of the medbay doors, eventually shaking his head as Jacob approached him, "Sir, is he going to be alright?" Shephard just stood there before giving a shrug of his shoulders, "I don't know. Mordin and Doctor Chakwas look like they'll be fine in there handling him."

Jacob nodded before pointing out, "Sir, the Illusive Man wants to see you for a mission report." Shephard nodded, then motioned for Jacob to follow.

During the entire report Shephards mind was…..elsewhere. Like he was more focused on what was happening down in the medbay. The Illusive Man took no notice, ending the report before the doors to the conference room slid open. The freshly scarred turian that walked through merely glanced at Jacob before looking to Commander Shephard, "Nobody would give me a mirror. How bad is it?"

Shephard just sighed before admitting, lightheartedly, "Oh hell, Garrus, you were always ugly. Slap some face paint on there and no one will even notice."

* * *

Calibrations. It was always a good excuse. It usually allotted the turian the down time that he wanted, save for the times Shephard came to talk or discuss strategy, or just generally bullshit around. Instead of heading right for the main battery though he decided to do the one unexpected thing and step in to speak with none other than the crews second-in-command. The crew that he happened to walk by stared briefly before smiling, or just going about their business as usual. It could have been worse, in truth.

The XO's doors opened up and Garrus stared furtively at Miranda, his mandibles twitching slightly as Miranda looked up before motioning for Garrus to take a seat, "Is there something I can help you with, Garrus?"

The question was to the point, at least. The turian sat down before shifting uncomfortably in his seat as he asked, "I did not realize Cerberus doctors were so….detailed about turian physiology. I was curious if this was something Cerberus was doing lately, or if your doctor in there was just being more open-minded with how things preceded?"

Miranda stared Garrus, her expression betraying mostly boredom, possibly a hint of curiosity as Garrus brought the subject up. She'd calmly clasp her fingers together, almost adopting a corporate style tone in her voice as she stated, "We at Cerberus feel it necessary to maintain knowledge as it is one of the biggest contributors to keeping humanity alive. In short, if one doctor feels it necessary to learn the workings of another, then perhaps humanity will be better off for it. Suffice to say I actually did not know Dr. Chakwas was well-maintained in alien races, especially their make-up, but it served to keep you alive, didn't it?"

Garrus narrowed his eyes, only slightly before shaking his head, "All you did was give me complete bullshit I already half-knew. If you didn't know you could have just said so." Garrus noticed that the XO's hands were back to typing away a report, though this did draw an uneasy feeling in the turian. Something now felt wrong, somehow. Like the atmosphere had changed based on the si—damn.

The turians mandibles flared, causing Miranda to notice, though she merely raised an eyebrow before asking, "Whatever the case, you're alive. Unless you have a complaint about a Cerberus doctor saving your life?"

Garrus just sat in mired silence, before slowly standing. His face hurt like hell as it was and he was advised to do as little talking as possible by the doctor. It was through the small connections that he could see what was happening. His inquiry was now being relayed to the Illusive Man, and at some point the doctor may suffer for it. This did not sit well. Garrus just gave Miranda a silent nod before exiting her quarters, his footsteps taking him through the kitchen, only to stop briefly and look towards the medbay. He could see the human doctor talking with Professor Solus before the latter exited, exclaiming, "Tests to do! Talk later!"

Doctor Chakwas was in his chair before looking up and realizing Garrus was staring at him. Without waiting for an invite the man was already standing up and through the doors of the medbay before approaching Garrus, "If you are going to be stubborn about not staying in the medbay then at least let me apply one more dose of medi-gel. It will at least ease the healing."

Garrus sighed before realizing a tiny thought. He sounded somewhat like his mother, scolding and bargaining to get what she wanted. She usually did. It took some weight off of Garrus's mind before he nodded, and stayed still as the doctor set about applying a new batch of medi-gel. Thankfully, the doctor was quiet as he worked, and hadn't scolded the young turian either.

"You do realize I don't have enough medi-gel if you keep up these kind of firefights, correct?"

Scratch that.

Garrus just gave the doctor a turian version of a human grin before responding in kind, "Then I hope we'll be making enough stops for you to restock often."

The doctor took that time to take out a pair of miniature binoculars(Garrus couldn't help but stare at them suspiciously) before it was first explained, "They're glasses, only modified." He pushed the glasses up the bridge of his nose before tapping a button on the side of them as he said, "Thankfully you heal fast. But I suppose I better go restock on what I can." His tone wasn't disapproving, more light and almost a hint of laughter in there.

It was then that Garrus remembered his conversation with Miranda. The former C-Sec officer wanted to warn the doctor about Miranda, and loyal to Cerberus or not, he deserved to know. Garrus tapped his omni-tool a few times before giving the doctor a nod, "I'll be in the Main Battery, catching up on calibrations if I'm needed." The doctor was already looking at his omni-tool as he said, "Please try not to talk to the main battery. It'll give your face time to heal." before walking off towards the medbay.

Whether he heeded Garrus's brief warning or not was now up to him. It couldn't hurt to keep an eye on the doctor in the meantime. Miranda Lawson, however, was an enigma. Garrus didn't like it.

* * *

Miranda finished filing the report she had been working on. Her evening had been uneventful mostly, save for the unexpected conversation with Garrus. She wouldn't admit to it but she was surprised that Dr. Chakwas had any knowledge of turian physiology at all. It made him suspect, and so she sent a report stating to the Illusive Man that she would be keeping a close eye on him. She had, of course, read his file multiple times, and knowing that he was an expert at hand to hand combat seemed off-putting to her.

A doctor that could fight? That was probably understandable in a field medic, but she couldn't recall reading over any mission reports where Dr. Chakwas had been in the field. The Illusive Man didn't seem to care, so long as the results were satisfactory. Luckily, they usually were.

Miranda would just lean back, taking a second to stretch, the tight catsuit kissing her skin as she yawned softly. Eventually she'd go back to filing reports for the moment before an idea occurred to her. She typed a few words into her omni-tool before resuming her work. Jacob should be coming to see her soon, now. With that, she could test out her idea, if it worked.

* * *

Joker sat in his seat, finally having silenced EDI, if just for the moment. Shephard had bothered him for a bit earlier, catching up on the good old days before trekking off to do who knows what. Joker, in the meantime, was getting stir-crazy. Even though EDI reprimanded him for any little thing and he could only tell her to shut up only so many times. At least, that was all before he found the mute button. He needed to go thank the guy who invented that brilliant device.

"Hello, Mr. Moreau."

Joker startled, surprised he had not heard the doctor coming. He turned his seat around in time to see the doctor standing there, right hand conspicuously behind his back and his left hand pushing a pair of glasses up the bridge of his nose. The look the doctor was giving him wasn't sadistic. But it was close. Joker suddenly realized one thing: Doctor Chakwas(like his mother) could be very intimidating.

The pilot was more worried about what was behind the doctors back, even as the young doctor stated, "I believe it's time for your medicine, Joker." Chakwas would then pull his right hand out to reveal a needle, to which Joker stiffened. He hated needles. And ever since he and the doctor had become sort-of pals the doctor seemed to have taken partial liberty with coming directly to Joker to administer his shots when they were needed.

Of course, that was only during downtime.

Of which they were on. Right now.

Dr. Chakwas took one step towards Joker, the pilot shifting uncomfortably in his seat before the doctor took another menacing step towards Joker. One more step would have Joker within easy reach, but Joker was already coming up with ideas in his head on how to elude the doctor, if just for the moment. He started off with light flailing, which worked, before triumphantly shouting at the doctor, "Ha! If your old lady couldn't get me to regularly take my meds, then you stand no chance."

For his credit the doctor just smiled before holding the needle up, tip pointed to the roof, before he pressed lightly, letting a small amount of liquid out as he said, "Is that so….?" The doctors eyes almost glinted at the challenge.

Joker gulped.

* * *

Jacob Taylor went about cleaning and prepping the weapons in the armory for the next mission. He still couldn't believe what went down on Freedom's Progress. The Commander knew his stuff, that was for sure. He moved, -really- moved on the battlefield. It was almost scary to watch. Sure, Miranda was there too, and Jacob was doing his thing, but Shephard was the one who easily stole the show. Granted, since Freedoms Progress he hadn't been on a mission with Shephard(aside from recruiting both the salarian and the turian) so Jacob was slightly anxious to see some combat again.

"Mr. Taylor, Commander Shephard is requesting you be ready for the next mission." EDI chimed in at the perfect time.

Jacob breathed a sigh of relief before asking, "Any idea what the mission is?"

"It appears that a ship is rapidly descending in orbit over a planet and will likely crash into a colony without intervention."

Wait, what?

He was about to inquire further when his omni-tool lit up with a message from none other than Ms. Lawson herself.

He read the message plaintively, unsure of why she would be asking something so….odd. Jacob quickly keyed in his response before looking back to the display console, "EDI, who else is going on the mission with us?"

"Commander Shephard has not yet decided, though it is likely between Professor Solus and Garrus Vakarian." was the reply given by the AI.

Jacob thought it over before nodding, "Actually, can you tell him I have a suggestion…."

* * *

**A/N: Wow. It took me –forevah- to finish this chapter. Personally, I'm blaming laziness, procrastination, and FF14: AWR. Take your pick. Anyway, R&R if you'd be so kind!**

**One thing I need to point out is the difference in story telling between the first and second part. I'm debating on re-writing the first part since I like how the second part flows as a story, but suggestions are always welcome.**


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